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TitleAlphaFold2 structures guide prospective ligand discovery.
Journal, issue, pagesScience, Vol. 384, Issue 6702, Page eadn6354, Year 2024
Publish dateJun 21, 2024
AuthorsJiankun Lyu / Nicholas Kapolka / Ryan Gumpper / Assaf Alon / Liang Wang / Manish K Jain / Ximena Barros-Álvarez / Kensuke Sakamoto / Yoojoong Kim / Jeffrey DiBerto / Kuglae Kim / Isabella S Glenn / Tia A Tummino / Sijie Huang / John J Irwin / Olga O Tarkhanova / Yurii Moroz / Georgios Skiniotis / Andrew C Kruse / Brian K Shoichet / Bryan L Roth /
PubMed AbstractAlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ and serotonin 2A (5- ...AlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ and serotonin 2A (5-HT2A) receptors, testing hundreds of new molecules and comparing results with those obtained from docking against the experimental structures. Hit rates were high and similar for the experimental and AF2 structures, as were affinities. Success in docking against the AF2 models was achieved despite differences between orthosteric residue conformations in the AF2 models and the experimental structures. Determination of the cryo-electron microscopy structure for one of the more potent 5-HT2A ligands from the AF2 docking revealed residue accommodations that resembled the AF2 prediction. AF2 models may sample conformations that differ from experimental structures but remain low energy and relevant for ligand discovery, extending the domain of structure-based drug design.
External linksScience / PubMed:38753765 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 3.0 Å
Structure data

42676

8uwl

EMDB-42676, PDB-8uwl:
5-HT2AR bound to Lisuride in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
Method: EM (single particle) / Resolution: 2.8 Å

42999

8v6u

EMDB-42999, PDB-8v6u:
5HT2AR-miniGq heterotrimer in complex with a novel agonist obtained from large scale docking
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-H8G:
N,N-diethyl-N'-[(8alpha)-6-methyl-9,10-didehydroergolin-8-yl]urea / medication*YM


ChemComp, No image

ChemComp-YEQ:
Unknown entry

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / 5-HT2A receptor / serotonin receptor / G protein / GPCR / Lisuride / cryoEM / active state GPCR / heterotrimer / complex / serotonin

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